rs6644575

Variant names:

• chrX-745504-C-T
• rs6644575

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.131 in 152,058 control chromosomes in the GnomAD database, including 1,432 homozygotes. There are 9,834 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.13 (1432 hom., 9834 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19980 AN: 151940 Hom.: 1434 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0887

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.125

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.131 AC: 19992 AN: 152058 Hom.: 1432 Cov.: 32 AF XY: 0.132 AC XY: 9834 AN XY: 74308

African (AFR) AF: 0.177 AC: 7325 AN: 41454

American (AMR) AF: 0.0885 AC: 1353 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 420 AN: 3472

East Asian (EAS) AF: 0.185 AC: 954 AN: 5160

South Asian (SAS) AF: 0.166 AC: 801 AN: 4812

European-Finnish (FIN) AF: 0.122 AC: 1289 AN: 10572

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7514 AN: 67986

Other (OTH) AF: 0.123 AC: 260 AN: 2112

Bravo AF: 0.129

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.86
PhyloP100		-1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6644575; hg19: chrX-706239;